Fig. 2

Patient PC63 showing biopsies, mNGS pathogen/CNV results, and orthogonal confirmation. A Schematic of the biopsies performed. B–D Histology of the bone marrow, paratracheal lymph node, and lung wedge biopsy show increased eosinophils (arrowheads) that were morphologically normal and indistinguishable from reactive and benign eosinophils. E Bacterial profile from mNGS testing. No viral, fungal, or parasitic pathogens were detected. F Copy number plotting across the human genome derived from metagenomic sequencing data. Six chromosomal scale deletions and duplications are identified, 3 of which accounted for > 90% of the human DNA content. G FISH (fluorescence in situ hybridization) of wedge biopsy, confirming presence of matching clonal complex cytogenetics to BAL fluid in F. Scale bar, 5 μm. H Bone marrow biopsy, confirming presence of matching clonal complex cytogenetics to BAL fluid in F